RetrogeneDB ID: retro_mmus_2594

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:107962133..107962312(+)
• Located in intron of: ENSMUSG00000029270

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Rpl37a
• Ensembl ID: ENSMUSG00000046330
• Aliases: None
• Description: ribosomal protein L37a [Source:MGI Symbol;Acc:MGI:98068]

Sequence

>retro_mmus_2594
GAGATCAGCTAGCACACCAAGTACACTTGTCCCATCCATGGCAAGACCACGATGAGGAGACGAGCCAATAGCATGGGGCA
CTGTGGCTCCGTGACAGAAAACAAGGGCTGGACCTATAATATCTCTCTACTGTCAAACTCAAGTCTGCCATCAGAAGACT
CAAGGTACTGAAAGACCAG

Alignment

ORF - retro_mmus_2594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.81 %
• Parental protein coverage: 68.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EISQHAKYTCSFCGKTKMKRRAVGIWHCGSCMKTVAGGAWTYNTT-SAVTVKSAIRRLKELKDQ
          EIS.H.KYTC...GKT.M.RRA....HCGS.........WTYN...S.V..KSAIRRLK.LKDQ
Retrocopy EIS*HTKYTCPIHGKTTMRRRANSMGHCGSVTENKG---WTYNIS<STVKLKSAIRRLKVLKDQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	32.45 RPM
SRP007412_cerebellum	0.04 RPM	19.41 RPM
SRP007412_heart	0.00 RPM	39.16 RPM
SRP007412_kidney	0.02 RPM	39.62 RPM
SRP007412_liver	0.00 RPM	35.64 RPM
SRP007412_testis	0.00 RPM	37.83 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_2594 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	5:107960700..107961798
ENCFF001YJZ	POLR2A	5:107960613..107962265
ENCFF001YKA	POLR2A	5:107959629..107962237

EST

No EST(s) were mapped for retro_mmus_2594 retrocopy.

TSS

No TSS is located nearby retro_mmus_2594 retrocopy 5' end.

Lab

retro_mmus_2594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2594 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 243 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003846	9 retrocopies	retro_btau_1039, retro_btau_1070, retro_btau_1083, retro_btau_1240, retro_btau_1269, retro_btau_1366, retro_btau_1531, retro_btau_382, retro_btau_437,
Choloepus hoffmanni	ENSCHOG00000004000	14 retrocopies	retro_chof_1281, retro_chof_1338, retro_chof_1734, retro_chof_1744, retro_chof_1839, retro_chof_1866, retro_chof_1885, retro_chof_2338, retro_chof_2566, retro_chof_2645, retro_chof_298, retro_chof_731, retro_chof_814, retro_chof_885,
Felis catus	ENSFCAG00000027010	21 retrocopies	retro_fcat_1001, retro_fcat_1070, retro_fcat_1099, retro_fcat_1221, retro_fcat_1343, retro_fcat_1364, retro_fcat_1403, retro_fcat_149, retro_fcat_1644, retro_fcat_1662, retro_fcat_1704, retro_fcat_1738, retro_fcat_1756, retro_fcat_1850, retro_fcat_1918, retro_fcat_1940, retro_fcat_2018, retro_fcat_271, retro_fcat_595, retro_fcat_612, retro_fcat_633,
Homo sapiens	ENSG00000197756	6 retrocopies	retro_hsap_1086, retro_hsap_2482, retro_hsap_3542, retro_hsap_3773, retro_hsap_764, retro_hsap_926,
Gorilla gorilla	ENSGGOG00000014827	5 retrocopies	retro_ggor_1546, retro_ggor_2393, retro_ggor_2538, retro_ggor_2636, retro_ggor_633,
Latimeria chalumnae	ENSLACG00000011578	1 retrocopy	retro_lcha_71,
Monodelphis domestica	ENSMODG00000025485	9 retrocopies	retro_mdom_1106, retro_mdom_1555, retro_mdom_1848, retro_mdom_1934, retro_mdom_350, retro_mdom_521, retro_mdom_771, retro_mdom_805, retro_mdom_975,
Mus musculus	ENSMUSG00000046330	18 retrocopies	retro_mmus_1036, retro_mmus_1764, retro_mmus_1979, retro_mmus_1993, retro_mmus_2070, retro_mmus_2114, retro_mmus_2594 , retro_mmus_2768, retro_mmus_3010, retro_mmus_3130, retro_mmus_322, retro_mmus_3367, retro_mmus_350, retro_mmus_508, retro_mmus_577, retro_mmus_589, retro_mmus_699, retro_mmus_830,
Nomascus leucogenys	ENSNLEG00000007276	8 retrocopies	retro_nleu_129, retro_nleu_1621, retro_nleu_1926, retro_nleu_2271, retro_nleu_2623, retro_nleu_271, retro_nleu_396, retro_nleu_406,
Ochotona princeps	ENSOPRG00000004436	10 retrocopies	retro_opri_1043, retro_opri_1060, retro_opri_1188, retro_opri_260, retro_opri_318, retro_opri_430, retro_opri_471, retro_opri_864, retro_opri_870, retro_opri_994,
Petromyzon marinus	ENSPMAG00000000001	1 retrocopy	retro_pmar_11,
Pongo abelii	ENSPPYG00000025878	1 retrocopy	retro_pabe_62,
Pan troglodytes	ENSPTRG00000029029	6 retrocopies	retro_ptro_1436, retro_ptro_2408, retro_ptro_2558, retro_ptro_535, retro_ptro_642, retro_ptro_738,
Sarcophilus harrisii	ENSSHAG00000013417	10 retrocopies	retro_shar_133, retro_shar_197, retro_shar_246, retro_shar_322, retro_shar_339, retro_shar_460, retro_shar_466, retro_shar_605, retro_shar_611, retro_shar_642,
Tupaia belangeri	ENSTBEG00000007409	108 retrocopies	retro_tbel_1089, retro_tbel_1095, retro_tbel_1113, retro_tbel_1168, retro_tbel_1198, retro_tbel_1204, retro_tbel_1218, retro_tbel_1244, retro_tbel_1345, retro_tbel_1352, retro_tbel_141, retro_tbel_1434, retro_tbel_1466, retro_tbel_1471, retro_tbel_148, retro_tbel_1489, retro_tbel_1502, retro_tbel_151, retro_tbel_1534, retro_tbel_1683, retro_tbel_1714, retro_tbel_1807, retro_tbel_1835, retro_tbel_1838, retro_tbel_1922, retro_tbel_194, retro_tbel_1973, retro_tbel_1992, retro_tbel_1995, retro_tbel_2002, retro_tbel_2044, retro_tbel_2083, retro_tbel_209, retro_tbel_2101, retro_tbel_2178, retro_tbel_2190, retro_tbel_223, retro_tbel_2381, retro_tbel_2631, retro_tbel_2699, retro_tbel_2705, retro_tbel_2725, retro_tbel_2780, retro_tbel_2813, retro_tbel_2844, retro_tbel_285, retro_tbel_286, retro_tbel_2985, retro_tbel_3022, retro_tbel_3048, retro_tbel_3108, retro_tbel_3118, retro_tbel_3211, retro_tbel_3490, retro_tbel_350, retro_tbel_3565, retro_tbel_3593, retro_tbel_3632, retro_tbel_3641, retro_tbel_3651, retro_tbel_3757, retro_tbel_3784, retro_tbel_3837, retro_tbel_3901, retro_tbel_3910, retro_tbel_3912, retro_tbel_3916, retro_tbel_3919, retro_tbel_3955, retro_tbel_3969, retro_tbel_3970, retro_tbel_4055, retro_tbel_4098, retro_tbel_4099, retro_tbel_4117, retro_tbel_412, retro_tbel_4148, retro_tbel_4188, retro_tbel_420, retro_tbel_4244, retro_tbel_4382, retro_tbel_4452, retro_tbel_4522, retro_tbel_4524, retro_tbel_458, retro_tbel_4586, retro_tbel_4588, retro_tbel_4613, retro_tbel_4703, retro_tbel_472, retro_tbel_500, retro_tbel_566, retro_tbel_574, retro_tbel_583, retro_tbel_590, retro_tbel_594, retro_tbel_595, retro_tbel_622, retro_tbel_648, retro_tbel_681, retro_tbel_739, retro_tbel_767, retro_tbel_790, retro_tbel_834, retro_tbel_870, retro_tbel_893, retro_tbel_907, retro_tbel_998,
Tarsius syrichta	ENSTSYG00000004258	11 retrocopies	retro_tsyr_1122, retro_tsyr_1704, retro_tsyr_1707, retro_tsyr_1831, retro_tsyr_1999, retro_tsyr_213, retro_tsyr_278, retro_tsyr_316, retro_tsyr_321, retro_tsyr_800, retro_tsyr_815,
Vicugna pacos	ENSVPAG00000002529	5 retrocopies	retro_vpac_208, retro_vpac_240, retro_vpac_271, retro_vpac_307, retro_vpac_479,